It should compile your file (if needed), copy it to the Beagle and start gdb on it. However I haven't been able to make it work.

Fix: The first time you try to select the Remote Absolute File Path for C/C++ Application you haven't uploaded the binary file to the Beagle. Hence you cannot select it via the dialogue. Once you clicked the "Debug" button you can re-open the dialogue and select the binary or you can manually complete the line to "/home/MyUsername/workspace/HelloWorld/Debug/HelloWorld".

Back when I had this working, it will run up to main() and wait for your input. Try the single step button (F6 step over, F5 step into)